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Hands-on training at EBI - Joint EMBRACE-EBI workshop: understanding protein structures

Course Summary
Course Details EMBRACE logo Title: Joint EMBRACE-EBI workshop: understanding protein structures
Date: 17-20 February 2009
Venue: Hinxton, Cambridge, UK
Organisers: Christine Orengo & James Watson
Admin Support: Alison Barker & Janet Copeland
Registration Deadline: 17th December 2008
Payment Deadline: 16th January 2009

About this Course


As part of its training program, the European Network of Excellence EMBRACE runs regular advanced courses on bioinformatics tools and services. This course, run in partnership with the European Bioinformatics Institute (EBI) as part of its training programme, will provide instruction and hands-on training in protein structures using several public databases and bioinformatics tools freely available on the internet. The course is aimed at novices who wish to find out about protein structure and how it relates to their own research, as well as researchers already familiar with protein structure who wish to find out about new ways to analyse and present their data.

Registration Closed.

Cost


There is a maximum number of 30 participants. This is a residential course, without exception, however the costs of the accommodation and catering have been heavily subsidised with funds from the EMBRACE network. There is a fee of £120 which includes all accommodation and food for the duration of the course (Tuesday 17th, evening registration 16:00, till Friday 20th 17:30). The registration deadline for this course is Wednesday 17th December 2008. There will then be a selection process and those successful will be emailed by Friday 19th December with payment details. The course fee must be paid before 16th of January 2009 otherwise the place will be offered to another participant.


There are a limited number of bursaries available which have been kindly provided by Rigaku Corporation. These would cover the cost of the registration fee but not travel. If you are intending to apply for such a bursary please indicate this on the registration form. You will then be contacted to provide supporting evidence and statements for your application.

Topics include


Searching for structures in the PDB and their schematic display; exploring the structural classification of proteins in the CATH and SCOP databases; identifying similar folds in the databases; examining the 3-D orientation of catalytic residues; identifying functional residues and patterns in the data; investigating small molecules bound to macromolecular structures; linking functional annotation to structures; investigating membrane proteins; studying and visualising protein interactions; homology modelling; and communicating information using protein structure.

Additional Sponsors


This meeting has received additional support from:

ENFIN logo

Rigaku logo





Trainers



James Watson
James
Watson

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Vicky Schneider
Vicky
Schneider

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Nicholas Furnham
Nicholas
Furnham

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Gemma Holliday
Gemma
Holliday

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Jennifer McDowall
Jennifer
McDowall

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Samuel Kerrien
Samuel
Kerrien

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Adel Golovin
Adel
Golovin

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Eugene Krissinel
Eugene
Krissinel

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Marialuisa Pellegrini-Calace
Marialuisa
Pellegrini-Calace

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Paula de Matos
Paula
de Matos

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Guest Speakers


  • Christine Orengo
  • Gert Vriend
  • Teresa Attwood
  • Daniel Kahn
  • Michael Tress
  • Jaime Prilusky
  • Eran Hodis
  • Oliver Redfern


Program Contents

The course content is now available to download for people who attend the course.

Time Topic
Day 1 - Tue 17th Feb 2009
16:00 - 18:00 Registration
19:00 - 22:00 Social Gathering
Day 2 - Wed 18th Feb 2009
09:00 - 09:30 Introduction to the EBI and EMBRACE
09:30 -10:45 Searching for structures and using molecular graphics viewers (James Watson and Vicky Schneider)
10:45 - 11:00 Coffee break
11:00 - 12:30 Folds, Families and Structure comparison (Christine Orengo and Oliver Redfern)
12:30 - 13:30 Lunch
13:30 - 14:30 Patterns: InterPro (Jennifer McDowall)
14:30 - 15:30 PRINTS (Teresa Attwood)
15:30 - 15:45 Coffee break
15:45 - 16:45 PRODOM (Daniel Kahn)
16:45 - 17:45 UTOPIA and CINEMA (Teresa Attwood)
19:00 - 22:00 Evening Course Dinner
Day 3 - Thu 19th Feb 2009
09:30 - 10:30 Structural motifs and active sites: Introduction to templates and Tempura (James Watson)
10:30 - 10:45 Coffee break
10:45 - 11:45 Structural motifs and active sites: Catalytic Site Atlas (Nicholas Furnham)
11:45 - 12:30 Structural motifs and active sites: PDBeMotif (Adel Golovin t.b.c.)
12:30 - 13:30 Lunch
13:30 - 14:30 TreeDet and FireDB (Michael Tress)
14:30 - 15:30 Enzymes: MACiE (Gemma Holliday)
15:30 - 15:45 Coffee break
15:45 - 16:30 Enzymes: IntEnz (Paula de Matos)
16:30 - 17:30 Small molecules: ChEBI (Paula de Matos)
Day 4 - Fri 20th Feb 2009
09:30 - 10:15 Assemblies and interactions: IntAct and PDBe (Samuel Kerrien)
10:15 - 11:00 Assemblies and interactions: MSDpisa (Eugene Krissinel)
11:00 - 11:15 Coffee break
11:15 - 12:15 Membrane Proteins (Marialuisa Pelligrini-Calace)
12:15 - 13:15 Lunch
13:15 - 14:00 Protein function from structure (James Watson)
14:00 - 15:00 From sequence to structure: Homology modelling (Gert Vriend)
15:00 - 15:15 Coffee break
15:15 - 16:45 Protein structure PR: Communicating information with Proteopedia (Jaime Prilusky and Eran Hodis)
16:45 - 17:00 Course survey and questions




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